Cyclists need to be removed from the road and then ''actively cross a side road'' as a pedestrian would, this being a crude example the sort;
Cycle lanes need to be separate from the roads. If using a section of road is the only option, then there should be a kerb at least separating the two (and preferably a railing).
The solutions in my town are ideal, but engineered-in. They can't easily be added into densely-built establishment. But there's still something to be said for bridges and underpasses.
We use roundabouts wherever possible, as they're quicker and safer than traffic lights. Our cycleways mostly use underpasses but there are a few junctions using bridges. The underpasses are better though, safer and can be very compact, they really should be engineered into any new junctions built...
Underpasses:
Bridges: